[BioC] edgeR: what to do with no replicates

[Gordon K Smyth]

Dear Bogdan,

The advice in the edgeR User's Guide about using estimateGLMCommonDisp() 
with method="deviance",robust="TRUE",subset=NULL is intended to be used 
without a design matrix, or in conjunction with the immediately preceding 
advice about removing terms from the design matrix.

I have now rewritten the advice in the User's Guide a little to make this 
more explicit.

Best wishes
Gordon

> Message: 2
> Date: Mon, 21 Nov 2011 12:41:05 -0800
> From: Bogdan Tanasa <tanasa at gmail.com>
> To: Mark Robinson <mark.robinson at imls.uzh.ch>
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] edgeR
>
> Hi Mark,
>
> I have two samples "Y" and "S" (with no replicates), and following edgeR
> manual on "what to do if you do not have replicates", I am getting the
> following results below. The end message is "No residual df: cannot
> estimate dispersion". Please could you let me know what is going wrong ..
> Thanks a lot !
>
>> raw.data <- read.delim("file")
>> d <- raw.data[,2:3]
>> rownames(d) <- raw.data[,1]
>
>> group <- factor(c("Y","S"))
>> design <- model.matrix(~group)
>> d <- DGEList(counts = d, group=group)
> Calculating library sizes from column totals.
>> dim(d)
> [1] 4013    2
>> d <- calcNormFactors(d)
>> d
> An object of class "DGEList"
> $samples
>  group lib.size norm.factors
> Y     Y   628062     1.049011
> S     S   422542     0.953279
>
> $counts
>                         Y   S
> chr8:53670099-53691880 132 109
> chr8:71033673-71122126 221 107
> chr8:74069636-74074658   7   1
> chr6:72172478-72187779 203 114
> chr6:72096548-72115900  36  15
> 4008 more rows ...
>
> $all.zeros
> chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
>                 FALSE                  FALSE                  FALSE
> chr6:72172478-72187779 chr6:72096548-72115900
>                 FALSE                  FALSE
> 4008 more elements ...
>
>>
> d<-estimateGLMCommonDisp(d,design,method="deviance",robust="TRUE",subset=NULL)
> Warning message:
> In estimateGLMCommonDisp.default(y = y$counts, design = design,  :
>  No residual df: cannot estimate dispersion
>
> For Common Dispersion (no GLM modeling):
>
>> d<-estimateCommonDisp(d,design)
> Warning message:
> In estimateCommonDisp(d, design) :
>  There is no replication.  Setting common dispersion to 0.
>> d
> An object of class "DGEList"
> $samples
>  group lib.size norm.factors
> Y     Y   628062     1.049011
> S     S   422542     0.953279
>
> $counts
>                         Y   S
> chr8:53670099-53691880 132 109
> chr8:71033673-71122126 221 107
> chr8:74069636-74074658   7   1
> chr6:72172478-72187779 203 114
> chr6:72096548-72115900  36  15
> 4008 more rows ...
>
> $all.zeros
> chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
>                 FALSE                  FALSE                  FALSE
> chr6:72172478-72187779 chr6:72096548-72115900
>                 FALSE                  FALSE
> 4008 more elements ...
>
> $common.dispersion
> [1] 1e-16
>
> $pseudo.alt
>                                Y         S
> chr8:53670099-53691880 103.192083 139.42506
> chr8:71033673-71122126 172.781586 136.86720
> chr8:74069636-74074658   5.453794   1.30187
> chr6:72172478-72187779 158.707305 145.81970
> chr6:72096548-72115900  28.129216  19.20588
> 4008 more rows ...
>
> $conc
> $conc.common
> chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
>          2.270073e-04           3.089534e-04           7.535477e-06
> chr6:72172478-72187779 chr6:72096548-72115900
>          2.985930e-04           4.803864e-05
> 4008 more elements ...
>
> $conc.group
>                                  S            Y
> chr8:53670099-53691880 2.706055e-04 2.003510e-04
> chr8:71033673-71122126 2.656403e-04 3.354361e-04
> chr8:74069636-74074658 2.482619e-06 1.062467e-05
> chr6:72172478-72187779 2.830186e-04 3.081155e-04
> chr6:72096548-72115900 3.723929e-05 5.464117e-05
> 4008 more rows ...
>
>
> $common.lib.size
> $pseudo
>                                Y         S
> chr8:53670099-53691880 103.192083 139.42506
> chr8:71033673-71122126 172.781586 136.86720
> chr8:74069636-74074658   5.453794   1.30187
> chr6:72172478-72187779 158.707305 145.81970
> chr6:72096548-72115900  28.129216  19.20588
> 4008 more rows ...
>
> $conc
> $conc.common
> chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
>          2.270073e-04           3.089534e-04           7.535477e-06
> chr6:72172478-72187779 chr6:72096548-72115900
>          2.985930e-04           4.803864e-05
> 4008 more elements ...
>
> $conc.group
>                                  S            Y
> chr8:53670099-53691880 2.706055e-04 2.003510e-04
> chr8:71033673-71122126 2.656403e-04 3.354361e-04
> chr8:74069636-74074658 2.482619e-06 1.062467e-05
> chr6:72172478-72187779 2.830186e-04 3.081155e-04
> chr6:72096548-72115900 3.723929e-05 5.464117e-05
> 4008 more rows ...
>
>
> $N
> [1] 515153
>
>
> On Fri, Nov 18, 2011 at 12:39 PM, Mark Robinson
> <mark.robinson at imls.uzh.ch>wrote:
>
>>
>>
>> On 18.11.2011, at 21:27, Bogdan Tanasa wrote:
>>
>>> Dear all,
>>>
>>> are the functions "estimateGLMCommonDisp" and "estimateGLMTagwiseDisp"
>>> available in edgeR on any platform ? I am using it on Linux/Ubuntu and
>>> apparently, these functiosn are not available.
>>
>>
>> What version of R/edgeR are you using?  Perhaps you have an old version?
>>  These functions have been around for awhile.  What does sessionInfo() give?
>>
>> Mark
>>
>>
>>
>>>
>>> thanks,
>>>
>>> Bogdan

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